RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease

Abstract

Despite the identification of several genetic factors linked to increased susceptibility to inflammatory bowel disease (IBD), underlying molecular mechanisms remain to be elucidated in detail. The ubiquitin ligases RNF20 and RNF40 mediate the monoubiquitination of histone H2B at lysine 120 (H2Bub1) and were shown to play context-dependent roles in the development of inflammation. Here, we aimed to examine the function of the RNF20/RNF40/H2Bub1 axis in intestinal inflammation in IBD patients and mouse models. For this purpose, intestinal sections from IBD patients were immunohistochemically stained for H2Bub1. Rnf20 or Rnf40 were conditionally deleted in the mouse intestine and mice were monitored for inflammation-associated symptoms. Using mRNA-seq and chromatin immunoprecipitation (ChIP)-seq, we analyzed underlying molecular pathways in primary intestinal epithelial cells (IECs) isolated from these animals and confirmed these findings in IBD resection specimens using ChIP-seq.The majority (80%) of IBD patients displayed a loss of H2Bub1 levels in inflamed areas and the intestine-specific deletion of Rnf20 or Rnf40 resulted in spontaneous colorectal inflammation in mice. Consistently, deletion of Rnf20 or Rnf40 promoted IBD-associated gene expression programs, including deregulation of various IBD risk genes in these animals. Further analysis of murine IECs revealed that H3K4me3 occupancy and transcription of the Vitamin D Receptor (Vdr) gene and VDR target genes is RNF20/40-dependent. Finally, these effects were confirmed in a subgroup of Crohn’s disease patients which displayed epigenetic and expression changes in RNF20/40-dependent gene signatures. Our findings reveal that loss of H2B monoubiquitination promotes intestinal inflammation via decreased VDR activity thereby identifying RNF20 and RNF40 as critical regulators of IBD.

Cell Type-Specific Induction of Inflammation-Associated Genes in Crohn’s Disease and Colorectal Cancer

“…For instance, TNFAIP3 in ILC1 and activated DC is induced by TNFα, as are IRF1 (and related interferon-pathway genes) in all of these cell types and STAT1 , leading to an autocrine loop of inflammation [ 38 ]. Similarly, the induction of HLA-C, which we have shown in all of these populations, can be explained via induction by TNFα [ 39 ]. The importance of these expression patterns is highlighted by the application of TNFα inhibitors as a mainstay therapy for over 20 years [ 40 , 41 , 42 ].…”

Histone Mono-Ubiquitination in Transcriptional Regulation and Its Mark on Life: Emerging Roles in Tissue Development and Disease

“…Treatment with a chemical carcinogen and DSS resulted in more colorectal polyps in Rnf20 +/− mice, which often progressed to inflammation-associated colorectal cancer [ 193 ]. In correspondence with these results, samples from human patients with ulcerative colitis, Crohn’s disease, and colorectal tumors, showed downregulation of RNF20/40 and H2BK120ub in both epithelium and stroma [ 193 , 200 ]. Similarly, when Rnf20 or Rnf40 were conditionally deleted in the mouse intestine, spontaneous colorectal inflammation occurred, and these knockout mice displayed significantly decreased survival [ 200 ].…”

“…In correspondence with these results, samples from human patients with ulcerative colitis, Crohn’s disease, and colorectal tumors, showed downregulation of RNF20/40 and H2BK120ub in both epithelium and stroma [ 193 , 200 ]. Similarly, when Rnf20 or Rnf40 were conditionally deleted in the mouse intestine, spontaneous colorectal inflammation occurred, and these knockout mice displayed significantly decreased survival [ 200 ]. Colon length was also decreased in these mice, and their colons showed severe epithelial damage and lymphoid infiltrates, while heterozygous Rnf20 or Rnf40 mice did not show similar phenotypes.…”

New Insights Into the Epigenetic Regulation of Inflammatory Bowel Disease

“…Besides, vitamin D condition was considered as one of the environmental or dietary associations with the activity of IBD ( Lim et al, 2005 ). And a study found that the monoubiquitination of histone H2B can promote the inflammation through decreased Vitamin D Receptor activity, and which maybe the biomarker of whether to receive Vitamin D supplements of IBD patients ( Kosinsky et al, 2021 ).…”